Research ArticleIdentification and Expression Analysis of Snf2 Family Proteins inTomato (Solanum lycopersicum)

Dongdong Zhang,1,2 Sujuan Gao,3 Ping Yang,1,2 Jie Yang,1,2 Songguang Yang ,1

and Keqiang Wu 4

1Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial KeyLaboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China2University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China3College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China4Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan

Correspondence should be addressed to Songguang Yang; yangsongguang@scbg.ac.cn and Keqiang Wu; kewu@ntu.edu.tw

Received 11 August 2018; Accepted 18 December 2018; Published 28 March 2019

Academic Editor: Michael Nonnemacher

Copyright © 2019 Dongdong Zhang et al. This is an open access article distributed under the Creative Commons AttributionLicense, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work isproperly cited.

As part of chromatin-remodeling complexes (CRCs), sucrose nonfermenting 2 (Snf2) family proteins alter chromatin structure andnucleosome position by utilizing the energy of ATP, which allows other regulatory proteins to access DNA. Plant genomes encode alarge number of Snf2 proteins, and some of them have been shown to be the key regulators at different developmental stages inArabidopsis. Yet, little is known about the functions of Snf2 proteins in tomato (Solanum lycopersicum). In this study, 45 Snf2swere identified by the homologous search using representative sequences from yeast (S. cerevisiae), fruit fly (D. melanogaster),and Arabidopsis (A. thaliana) against the tomato genome annotation dataset. Tomato Snf2 proteins (also named SlCHRs) couldbe clustered into 6 groups and distributed on 11 chromosomes. All SlCHRs contained a helicase-C domain with about 80 aminoacid residues and a SNF2-N domain with more variable amino acid residues. In addition, other conserved motifs were alsoidentified in SlCHRs by using the MEME program. Expression profile analysis indicated that tomato Snf2 family genesdisplayed a wide range of expressions in different tissues and some of them were regulated by the environmental stimuli such assalicylic acid, abscisic acid, salt, and cold. Taken together, these results provide insights into the functions of SlCHRs in tomato.

1. Introduction

In eukaryotes, about 147 bp of DNA wrapping around a his-tone octamer forms nucleosome, the fundamental unit ofchromatin. The reversible changes in chromatin structurealter the stability of the nucleosome, thereby facilitating reg-ulatory factors access, such as transcription factor [1, 2].Thus, the precise chromatin structure is essential for the cor-rect spatial and temporal gene expression in the eukaryotes[3, 4]. The changes in chromatin involve histone modifica-tions, DNA methylation, histone variants, and chromatinremodeling. Many proteins have been identified to mediatethese processes, among which the Snf2 family proteinscan affect gene expression by using the energy of ATP hydro-lysis to alter the interactions between histones and DNA

[5]. Indeed, most Snf2 proteins associated with other chro-matin remodelers form large multisubunit complexes calledchromatin-remodeling complexes, which most likely alterthe activity of the core ATPase in vivo. The accessory sub-units commonly contain additional domains that may affectthe enzymatic activity of the complex, facilitate its bindingto other proteins, and target the complex to DNA and/ormodified histones [6]. The chromatin-remodeling complexesare conserved throughout eukaryotes with essential roles inmany aspects of chromatin biology.

Based on the different protein compositions and func-tions, the chromatin-remodeling complexes can be dividedinto SWI/SNF, ISWI (imitation switch), INO80 (inositolrequiring 80), and CHD (chromodomain, helicase, andDNA binding) groups [7]. The SWI/SNF complexes alter

HindawiInternational Journal of GenomicsVolume 2019, Article ID 5080935, 15 pageshttps://doi.org/10.1155/2019/5080935

the position of the nucleosome at promoters, which canregulate transcription either positively or negatively [8].The ISWI group complexes were essential for chromatinassembly and the formation of nucleosome arrays withwell-ordered spacing, which might help to promote repres-sion [9]. In yeast, the ino80 mutants are defects in homolo-gous recombination during DNA repair, indicating thatthe INO80 complexes are involved in DNA repair [10].Indeed, the INO80 complexes could be recruited to double-stranded breaks (DSBs) via direct binding of the complexsubunits to phosphorylated H2AX or γ-H2AX [11, 12],which facilitates nucleosome eviction at DSBs, allowingthe recruitment of repair factors. In comparison, the CHDcomplexes have diverse functions. For instance, CHD1 istargeted to sites of active transcription through PHD-mediated recognition of H3K4me3 [13, 14] and associateswith other preinitiation factors to facilitate transcriptionalelongation and splicing [15]. In addition, CHD3 and CHD4are incorporated into a large protein complex with histonedeacetylases to repress transcription by binding to methyl-ated DNA in an MBD2/3-dependent manner, remodelingthe surrounding chromatin, and removing active histonemarks [16, 17].

SWI2/SNF2, the first Snf2 protein, was identified fromSaccharomyces cerevisiae by the examination of mating typeswitching (SWI) and sucrose nonfermenting (SNF) mutants[18]. Further data indicated that the SWI2/SNF2 gene ishomologous to a number of other ATP-binding helicases ofthe DEAD/H family [19]. The sequence similarity includesthe catalytic ATPase domain and seven characteristic proteinmotifs [20]. Moreover, the conserved domain analysis indi-cated that the helicase-like region can be further divided intotwo domains: the SNF2-N and helicase-C domains [21, 22].Based on the helicase-like region, the Snf2 family proteinsare grouped into six clades, including the Snf2-like, SWI/SN-F-related protein-like (Swr1-like), Rad54-like, Rad5/16-like,SSO1653-like, and Distant family [21].

Arabidopsis contains 41 Snf2 family proteins that fall into18 subfamilies [22]. The function of Arabidopsis BRAHMA(BRM) and SPLAYED (SYD), the closest homologs of yeastand animal SWI2/SNF2 ATPase subunits (Snf2 subfamily),has been investigated. Mutations of SYD cause defects ofthe shoot apical meristem (SAM). Furthermore, SYD physi-cally interacts with the promoter of WUSCHEL (WUS), acentral regulator in SAM [23]. The expression profile showedthat BRM was mainly expressed in the active cell divisiontissues, such as meristems and organ primordia [24]. TheBRM mutants displayed multiple developmental defects,such as reduced plant size and root length [24, 25], down-ward curling leaves [25], more sensitivity to abscisic acid(ABA) [26], and early flowering [27]. SYD and BRM wereshown to interact with LEAFY and SEPALLATA3 proteins,which are essential for floral organ identity [28]. Indeed,the functions of BRM to modulate gene transcription arealways through association with other nuclear proteins. Forexample, the plant-unique H3K27 demethylase, RELATIVEOF EARLY FLOWERING 6 (REF6), recruits BRM to itstarget genomic loci containing a CTCTGYTY motif [29].Moreover, FORGETTER1 (FGT1), which is specifically

required for the heat stress memory coactivator, maintainsits target loci in an open and transcription-competent stateby interacting with BRM near the transcriptional start site[30]. BRM also interacts with other transcription factorssuch as TEOSINTE BRANCHED1 CYCLOIDEA ANDPCF-CODING GENE (TCP4), ANGUSTIFOLIA3 (AN3),and BREVIPEDICELLUS (BP) to regulate gene expressioninvolved in leaf development and inflorescence architecture[31, 32]. A recent report showed that BRM also interactswith PHY-INTERACTING FACTOR 1 (PIF1) to modulatePROTOCHLOROPHYLLIDEOXIDOREDUCTASE C (PORC)expression, which is essential for chlorophyll biosynthesisduring the transition from heterotrophic to autotrophicgrowth [33]. Meanwhile, SUMOylation of BRM caused byMETHYL METHANE SULFONATE SENSITIVITY 21(MMS21) increases the BRM stability in root development[34]. Interestingly, more recent data demonstrated thatmicroRNA precursors (pri-miRNAs) are the substrates ofBRM. As a partner of the microprocessor component SER-RATE (SE), BRM accesses pri-miRNAs through SE andremodels their secondary structures, which prevents furtherdownstream processing mediated by DCL1 and HYL1 [35].

Transgenic Arabidopsis plants overexpressing AtCHR12,a member of the Snf2 subfamily, exhibit growth arrestof primary buds and growth reduction of the primary stemunder drought and heat stress [36]. Moreover, a Rad54-likefamily member, DEFECTIVE IN RNA-DIRECTED DNAMETHYLATION1 (DRD1), and a member of Snf2-like pro-tein, DECREASED DNA METHYLATION 1 (DDM1), areinvolved in DNA methylation [37, 38]. In addition, DRD1and DDM1 are also involved in leaf senescence, since drd1and ddm1 mutants exhibit a delayed leaf senescence pheno-type [39]. Furthermore, PHOTOPERIOD-INDEPENDENTEARLY FLOWERING 1 (PIE1), a Swr1 subfamily member,known to deposit histone H2A.Z, is also important forflowering and plant development [40, 41], while the Mi-2subfamily member PICKLE is a key regulator in brassi-nosteroid (BR), gibberellin (GA), and cytokinin (CK)signaling [42, 43].

Compared with Arabidopsis, little is known about Snf2proteins in other plant species. In rice, OsDDM1a andOsDDM1b, two genes homologous to Arabidopsis DDM1,are involved in DNA methylation [44], while rice CHR729,a member of the CHD3 family, plays an important role inseedling development via the GA signaling pathway [45].A previous study has also analyzed the DRD1 and Snf2subfamilies in tomato, which were reported to be involvedin stress responses [46]. In addition, constitutively overex-pressing a Snf2 gene (termed as SlCHR1, Solyc01g079690)caused reducing growth of transgenic tomato plants (cv.Micro-Tom) [47]. However, the largest and most diversegene family, the Snf2 gene family, has not been system-atically analyzed in the tomato genome. In this study,we identified and characterized 45 Snf2 family proteinsfrom tomato. The expression profiles of the tomato Snf2genes were also analyzed. The results provide a wealth ofinformation for further exploring the developmental func-tion of Snf2 family proteins in tomato, especially duringfruit development.

2 International Journal of Genomics

2. Materials and Methods

2.1. Plant Materials and Growth Conditions. In this study,the Solanum lycopersicum cultivar “Heinz 1706” was used asan experimental material. Surface-sterilized tomato seedswere grown in the Murashige and Skoog (MS) medium with1.5% sucrose and 0.8% agar for 14 days in a controlled envi-ronment greenhouse with a long photoperiod (16 h light/8 hdark) at 23 ± 1°C.

2.2. Identification of Tomato SlCHR Genes. The proteinsequences of AtCHRs from Arabidopsis thaliana, S. cere-visiae, and D. melanogaster were retrieved from ChromDB(http://www.chromdb.org). The deduced sequences ofSlCHR proteins in tomato were obtained as described else-where using the BLASTP program (https://solgenomics.net/tools/blast/, ITAG3.20). Then, the candidates of SlCHR pro-teins were confirmed using Pfam (http://pfam.xfam.org/)and SMART (http://smart.embl-heidelberg.de/) programs.The domain architecture was drawn using the DOG2.0software [48].

2.3. Chromosome Location and Sequence Feature Analyses.Chromosome location of SlCHR genes was determined byBLAST analysis of SlCHRs against SGN (http://solgenomics.net/organism/Solanum_lycopersicum/genome). The pro-gram DnaSP was used to carry out synonymous substitution(Ks) values of paralogous gene pairs [49]. The ComputepI/Mw tool on the ExPASy server (http://web.expasy.org/compute_pi/) was used to predicted molecular weight (Mw)and theoretical isoelectric point (pI) of SlCHRs. The struc-tures of SlCHR genes were predicted using the Gene Struc-ture Display Server (http://gsds.cbi.pku.edu.cn/) [50].

2.4. Phylogenetic Construction and Motif Analysis. The phy-logenetic trees were generated as described elsewhere usingMEGA5.2 program [51]. The Pfam program (http://pfam.xfam.org/) and Conserved Domain Database (CDD, http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) were usedto predict the conserved domains of SlCHRs. The 80amino acids of the helicase-C domain were aligned withClustalW. Sequence logos were generated using theWebLogo platform (http://weblogo.berkeley.edu/). Potentialprotein motifs were predicted using the MEME package(http://meme-suite.org/tools/meme).

2.5. Expression Data Visualization. The expression dataof tomato SlCHRs were extracted from publicly availableRNA-seq datasets from the Tomato Genome Consortium[52] and visualized with Matrix2PNG (http://www.chibi.ubc.ca/matrix2png/bin/matrix2png.cgi) [53]. The RNA-seqdata were obtained from transcriptome sequencing usingthree-week-old sand-grown seedlings, roots, leaves, buds(unopened flower buds), and flowers (fully open flowers) aswell as fruits (at 1 cM, 2 cM, and 3 cM), MG (mature green),breaker (B, early ripening), and 10-day post-B (B10, red ripe)stages of tomato “Heinz 1706.”

2.6. Gene Expression Analyses. For hormone and salt stressresponse test, 2-week-old tomato “Heinz 1706” seedlings

grown in the MS medium were transferred to the liquid MSmedium containing SA (1mM), ABA (50μM), and NaCl(200mM) for 4 h, respectively. For cold stress test, theplanes were transferred to a 4°C growth cabinet for 4 h.Total RNA from treated seedlings was extracted with TRIzolreagent (Invitrogen) according to the manufacturer’s proto-col and used to synthesize cDNA. Real-time PCR was per-formed with iTaq™ Universal SYBR® Green Supermix(Bio-Rad) using ABI 7500 Fast Real-Time PCR System. Thegene-specific primers for real-time PCR were designed byPrimer 3.0 [36] and listed in Supplemental Table 2. TomatoActin (Solyc03g078400) was served as an internal control.

3. Results

3.1. Identification of Snf2 Family Proteins in Tomato. Touncover the complete family of genes for encoding Snf2proteins in the tomato genome, iterative BLASTP researchesusing representative sequences from yeast (S. cerevisiae), fruitfly (D. melanogaster), and Arabidopsis (A. thaliana) wereconducted against SGN (http://solgenomics.net/organism/Solanum_lycopersicum/genome, ITAG3.20) genome anno-tation database. In total, 45 nonredundant putative Snf2genes were identified in the tomato genome (Table 1).

According to the current used nomenclature in Arabi-dopsis and rice, we designated Snf2 proteins of tomato(Solanum lycopersicum) as SlCHRs. All of the deducedSlCHR proteins contained the conserved SNF2-N domainand helicase-C domain. The theoretical isoelectric point(pI) of SlCHR candidates ranged from 5.13 to 9.42, andthe length of SlCHRs varied from 391 to 2500 aminoacids. The molecular weight (Mw) and the number ofintrons varied from 44.3 to 274.2 kDa and 1 to 37, respec-tively (Supplemental Table 1). Mapping SlCHRs to thetomato genome showed that 45 SlCHRs were unevenlydistributed on 11 chromosomes (except for chromosome10). Among them, there were 9 SlCHRs on Chr1; 5 on eachof Chr2 and Chr4; 3 on each of Chr6, Chr11, and Chr12; 4on each of Chr3 and Chr7; 2 on Chr5; 6 on Chr8; and oneon Chr9, respectively (Figure 1). Most SlCHRs were locatedin the bottom regions of tomato chromosomes, and fewwere in the central regions of chromosomes (Figure 1).

Moreover, 8 pairs of SlCHRs (Ks < 1 0) were evolvedfrom intrachromosomal duplication (Supplemental Figure 1and Table 2), indicating the importance of gene duplicationfor SlCHR gene expansion.

3.2. Phylogenetic Analysis of Snf2 Proteins in Tomato, Yeast,Fruit Fly, and Arabidopsis. In order to investigate theevolutionary relationship of Snf2 proteins in tomato,Arabidopsis (A. thaliana), yeast (S. cerevisiae), and fruit fly(D. melanogaster), a neighbor-joining (NJ) phylogenetic treewas constructed with 45 SlCHRs, 30 AtCHRs, 13 ScSnf2s,and 14 DmSnf2s using MEGA5.2. The results showed thatthe 45 SlCHR proteins were grouped into 6 clusters,namely, the Snf2-like (10 members), Swr1-like (4 members),SSO1653-like (3 members), Rad54-like (14 members), Dis-tant family (2 members), and Rad5/16-like (12 members).Additionally, each subfamily could be further divided into

3International Journal of Genomics

Table 1: Snf2 family genes in tomato and Arabidopsis.

Group Subfamily Arabidopsis thaliana Solanum lycopersicum Loc. symbol

Snf2-like

Chd1 CHR5 SlCHR45 Solyc12g099910

Mi-2 CHR6 (PICKLE) SlCHR27 Solyc06g054560

CHR4 SlCHR33 Solyc08g029120

CHR7

CHD7

Iswi CHR11 SlCHR2 Solyc01g067390

CHR17 SlCHR26 Solyc06g050510

Lsh CHR1 (DDM1) SlCHR14 Solyc02g062780

SlCHR13 Solyc02g085390

Snf2 CHR2 (BRM) SlCHR8 Solyc01g079690

CHR3 (SYD) SlCHR41 Solyc11g062010

CHR12 SlCHR6 Solyc01g094800

CHR23

ALC1

Swr1-like

Swr1 CHR13 (PIE) SlCHR17 Solyc03g063220

Ino80 CHR21 (Ino80) SlCHR19 Solyc04g016370

Etl1 CHR19 SlCHR10 Solyc02g014770

EP400 CHR10 SlCHR7 Solyc01g090650

SSO1653-like

Mot1 CHR16 SlCHR36 Solyc08g074500

ERCC6 CHR8 SlCHR39 Solyc09g066480

CHR24 SlCHR3 Solyc01g068280

SSO1653

Rad54-like

Rad54 CHR25 (RAD54) SlCHR22 Solyc04g056400

CHR9 SlCHR32 Solyc07g053870

Arip4

ATRX CHR20 SlCHR20 Solyc04g050150

JBP2 CHR38 SlCHR25 Solyc05g044510

CHR42

DRD1 CHR35 (DRD1) SlCHR9 Solyc01g109970

CHR34 SlCHR34 Solyc08g061410

CHR31 SlCHR35 Solyc08g062000

CHR40 SlCHR11 Solyc02g033050

SlCHR37 Solyc08g077610

SlCHR21 Solyc04g054440

SlCHR1 Solyc01g060460

SlCHR38 Solyc08g077690

SlCHR4 Solyc01g068300

SlCHR5 Solyc01g068320

DistantSMARCAL1 CHR14 SlCHR18 Solyc03g115520

CHR18 SlCHR44 Solyc12g098860

Rad5/16-like

SHPRH CHR39 SlCHR40 Solyc11g005250

CHR36

Lodestar

Ris1 CHR30 SlCHR12 Solyc02g050280

CHR33 SlCHR16 Solyc03g006570

CHR27 SlCHR24 Solyc05g044480

CHR28 SlCHR23 Solyc04g056410

CHR26 SlCHR31 Solyc07g052100

4 International Journal of Genomics

subgroups. For example, Rad54-like subfamily was furtherclassified into four subgroups, namely, Rad54, J-bindingprotein 2 (JBP2), alpha thalassemia/mental retardation syn-drome X-linked (ATRX), and DRD1, containing 2 (SlCHR22and SlCHR32), 1 (SlCHR25), 1 (SlCHR20), and 10 SlCHRs,respectively (Figure 2 and Table 1). Tomato possessed 10proteins belonging to the Snf2-like subfamily, which fell intothe chromodomain, helicase, and DNA binding (Chd1)(1 member); Mi-2 (2 members); Imitation SWI2 (Iswi)(2 members); lymphoid-specific helicase (Lsh) (2 members);

and Snf2 (3 members) subgroup, respectively (Figure 2 andTable 1).

Phylogenetic analysis showed that SlCHR6, SlCHR41,and SlCHR8 (also named as SlCHR1 in a recent report)displayed high sequence homology with Scsnf2 andDmBrahma, the ATPases of SWI/SNF-type chromatin-remodelingcomplex in yeast and fruit fly (Figure 2). Inaddition, 7 sister pairs (SlCHR2-SlCHR26, SlCHR6-SlCHR8,SlCHR34-SlCHR35, SlCHR11-SlCHR37, SlCHR4-SlCHR5,SlCHR23-SlCHR31, and SlCHR28-SlCHR29) were very likely

Table 1: Continued.

Group Subfamily Arabidopsis thaliana Solanum lycopersicum Loc. symbol

CHR37 SlCHR30 Solyc07g051970

CHR41 SlCHR28 Solyc06g065730

SlCHR29 Solyc07g051960

Rad5/16 CHR32 SlCHR15 Solyc03g005460

CHR29 SlCHR42 Solyc11g066790

CHR22 SlCHR43 Solyc12g020110

10 cM

SlCHR1

1 2 3

SlCHR2SlCHR3SlCHR4SlCHR5SlCHR6SlCHR7SlCHR8

SlCHR9

SlCHR10

SlCHR11

SlCHR12

SlCHR13

SlCHR14

SlCHR15SlCHR16

SlCHR17

SlCHR18

SlCHR19

SlCHR20

SlCHR21SlCHR22SlCHR21

SlCHR24SlCHR25

SlCHR26SlCHR27SlCHR28

SlCHR29SlCHR30SlCHR31SlCHR32

SlCHR33

SlCHR34SlCHR35SlCHR36SlCHR37SlCHR38

SlCHR39

SlCHR40

SlCHR41SlCHR42

SlCHR43

SlCHR44SlCHR45

4 5 6

7 8 9 10 11 12

Figure 1: Chromosomal location of SlCHR genes. The scale represents 10 centimorgans.

5International Journal of Genomics

to be paralogous proteins (Figure 2), while 20 pairs ofSlCHRs seemed to be orthologous proteins (Figure 2).Among these paralogous proteins, SlCHR2/26 and SlCHR6/8belonged to the Snf2-like subfamily and SlCHR34/35,SlCHR11/37, and SlCHR4/5 were from the Rad54-likesubfamily, whereas SlCHR23/31 and SlCHR28/29 were inthe Rad5/16-like subfamily (Figure 2). The wider paralogouspairs existed in SlCHR proteins, indicating that the expan-sion of SlCHR genes occurred after separation of paralogousgenes. Interestingly, in the unrooted phylogenetic tree basedon the data from Arabidopsis, rice, and tomato (Supplemen-tal Figure 2), two distinct branches in the DRD1 subfamilyand Ris1 subfamily were consisted of only SlCHRs. Thesedata indicated that expansion of DRD1 and Ris1 membersin tomato was most like due to gene duplication.

3.3. Comparative Analysis Gene Structures of SlCHR andAtCHR. Gene structure analysis of 45 SlCHR genes displayedthat the number of introns varied from 1 (SlCHR21, SlCHR4,SlCHR5, and SlCHR21) to 37 (SlCHR41) (Figure 3 andSupplemental Table 1). By contrast, the intron number of41 AtCHRs varied between 2 and 33 (Supplemental Table 1and Supplemental Figure 3). The length of introns alsovaried significantly among the SlCHR subfamily includingSnf2-like, Swr1-like, and Rad5/16-like genes (Figure 3).Interestingly, the distribution of intron phases in SlCHRswas very similar to AtCHRs (Supplemental Figure 4).

Next, we compared the internal exons and introns ofSlCHRs with those of AtCHRs. The results showed that theexons of SlCHRs varied 18 to 3067 bp with the average of215 bp, which was smaller than the average length of AtCHRexons (263 bp). Interestingly, most CHRs (about 86% ofSlCHR and 83% of AtCHR) had an exon with a size below300 bp (Figure 4(a)), while 56% of SlCHR exons and 53% ofAtCHR exons were between 60 and 160 bp (Figure 4(b)).

Although the size distribution of SlCHR exons was simi-lar to AtCHR exons, the size distribution of intron was morevariable, ranging from 34 bp to 9.0 kb. There were 54 SlCHRintrons (9.5%) with sizes > 1 5 kb; however, no such intronsexisted in AtCHRs (Figure 4(c)). About 61% of SlCHR and89% of AtCHR introns had sizes below 300 bp, while 56%of SlCHR introns were between 60 and 160 bp and 53% ofAtCHR introns were between 80 and 120 bp, respectively(Figure 4(c)). Meanwhile, the average sizes of SlCHR intronsand AtCHRs were 595 bp and 153 bp, respectively. Theseresults indicated that the exon and intron size distributionwas different between SlCHRs and AtCHRs.

3.4. The Conserved Motifs in SlCHRs. To investigate the con-served domains of SlCHRs, Pfam (http://pfam.xfam.org/)and Conserved Domain Database (CDD, http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) programs were used.The results showed that all the 45 SlCHRs contained ahelicase-C domain with about 80 amino acid residues and aSNF2-N domain with more variable amino acid residues(Figure 5).

Unlike the human Snf2 subfamily proteins hBRG1andhBRM, the conserved HSA (helicase-SANT-associated)domain was not found in all three Snf2 subfamily proteins(SlCHR8, SlCHR41, and SlCHR6) and only SlCHR8 con-tained bromodomain, an acetyl-lysine binding domain(Figure 5). However, an alignment profile using the HSAdomain of humans and the N-termini of SlCHR8, SlCHR41,and SlCHR6 showed that the conserved amino acid resi-dues including E, H, and L were found in tomato Snf2subfamily proteins (Supplemental Figure 5). Interestingly,the Swr1 subfamily SlCHR17 was highly homologous toArabidopsis PIE1, containing the HSA domain at theN-terminus (Figure 5). Furthermore, two members of theIswi subfamily, SlCHR2 and SlCHR26, had the conserveddomains HAND, SANT, and SLIDE located on the C-terminus (Figure 5). The Mi-2 subfamily proteins, SlCHR27and SlCHR33, contained two double chromodomains andan additional PHD domain at the N-terminal part of theproteins. All members of the Rad5/16-like family groupexcept SlCHR29 had a RING-finger E3 ubiquitin ligasedomain embedded between the SNF2-N and helicase-Cdomain in the C-terminal regions (Figure 5). Furthermore,an additional HIRAN domain was found in the N-terminalregion of SlCHR42 and SlCHR43 in this group. In general,the HIRAN domain was predicted to recognize featuresassociated with damaged DNA or stalled replication forks,such as ssDNA stretches or DNA lesions [54].

In addition to these conserved domains, other con-served motifs were searched using the MEME program.20 motifs for 45 SlCHRs were identified (Table 3). Thenumber of motifs in each SlCHR varied from 5 to 16(Table 3). Motifs 10, 4, and 1 were actually the helicase-Cdomain (Supplemental Figure 6) that was found in most ofthe SlCHRs. In addition to the conserved motifs, severalother motifs were also identified in SlCHR proteins, suchas motifs 13, 16, 20, 7, 8, and 18 in the DRD1 subfamilyas well as motifs 17, 14, 15, and 19 in the Rad5/16-likegroup (Table 3). Sequence analysis of helicase-C domains

Table 2: The nonsynonymous substitution (Ks) of SlCHRparalogous genes.

Paralogous genes Ks

SlCHR27 (Chr6)/SlCHR33 (Chr8) 1.030

SlCHR2 (Chr1)/SlCHR26 (Chr6) 1.360

SlCHR6 (Chr1)/SlCHR8 (Chr1) 0.860

SlCHR13 (Chr2)/SlCHR14 (Chr2) 0.172

SlCHR7 (Chr1)/SlCHR19 (Chr4) 0.840

SlCHR10 (Chr2)/SlCHR17 (Chr3) 1.500

SlCHR34 (Chr8)/SlCHR35 (Chr8) 0.285

SlCHR11 (Chr2)/SlCHR37 (Chr8) 1.085

SlCHR1 (Chr1)/SlCHR38 (Chr8) 0.177

SlCHR4 (Chr1)/SlCHR5 (Chr1) 0.107

SlCHR3 (Chr1)/SlCHR39 (Chr9) 1.290

SlCHR22 (Chr4)/SlCHR32 (Chr7) 0.729

SlCHR15 (Chr3)/SlCHR42 (Chr11) 0.550

SlCHR12 (Chr2)/SlCHR16 (Chr3) 1.465

SlCHR23 (Chr4)/SlCHR31 (Chr7) 1.238

SlCHR28 (Chr6)/SlCHR29 (Chr7) 1.346

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Iswi

Lsh

Snf2

Chd1

Chd7

Mi-2

Swr1

EP400

Ino80

Etl1

Mot1

MRCC6

Rad54

ATRX

JBP2

DRD1

SMARCAL1

SHPRH

Lodestar

Rad5/16

Ris1

Rad5/16-like

Distant

Rad54-like

SS01653-like

Swr1-like

Snf2-like

SICHR2SICHR26AtCHR11AtCHR17DmlswiScIswi2-Isw1ScLsh-IRCSICHR13SICHR14AtCHR1-DDM1AtCHR2-BRMSICHR41AtCHR3-SYDScSnf2DmbrahmaSICHR6SICHR8AtCHR12AtCHR23SICHR45AtCHR5DmChd1ScCHD1-Chd1DmCHD7-kismetAtCHR4DmMi-2AtCHR7SICHR33SICHR27

ScSwr1-Swr1DmSwr1-dominoSICHR17AtCHR13-PIE1SICHR7AtCHR10DmIno80ScIno80-Ino80SICHR19AtCHR21-lNO80ScEtl1-Fun30DmEtl1SICHR10

SICHR36AtCHR16DmMot1-Hel89BScMot1-Mot1SICHR3AtCHR24ScERCC6-Rad26SICHR39

SICHR32AtCHR9ScRad54-Rad54DmRad54-okraSICHR22AtCHR25-RAD54SICHR20AtCHR20DmArip4-CG4049DmATRX-XNPAtCHR38AtCHR42SICHR25SICHR9AtCHR35-DRD1AtCHR34AtCHR31AtCHR40SICHR34SICHR35SICHR11SICHR37SICHR21SICHR1SICHR38SICHR4SICHR5

SICHR18AtCHR14SICHR44

SICHR40

ScRad5/16-Rad5SICHR15AtCHR32SICHR42AtCHR29SICHR43AtCHR22ScRis1-ULS1AtCHR30AtCHR33SICHR16AtCHR27AtCHR28SICHR12AtCHR26AtCHR41SICHR24SICHR23SICHR31AtCHR37SICHR30SICHR28SICHR29

AtCHR39AtCHR36DmLodestar-Ids

AtCHR18

DmSMARCAL1-Marca1

AtCHR8

AtCHR19

AtCHR6-PICKLE

6299

4835

12

10

10

9

16

21

14

7

35

2693

49

100

34

36

67

56

99

9984

30

14

2828

3499

8266

9580

100100

3698

447636

16100100

4798

33

3897

99100

3299

86100100

8093

9899

79100

75

56

6499

47

45

93

29

25

2122

4348

10087

4699

10059

5897

3492

99

6996

43

7499

43

14

30

27

21

52

8839

89

40

3190

89

67

100

9965

62

Figure 2: Neighbor-joining (NJ) phylogenetic tree for Snf2s in S. cerevisiae (Sc), D. melanogaster (Dm), A. thaliana (At), and Solamumlycopersicum (Sl). The groups of homologous genes identified and bootstrap values are shown. The reliability of branching was assessed bythe bootstrap resampling method using 1,000 bootstrap replicates.

7International Journal of Genomics

identified the conserved acid residues such as Asp, Gly, Arg,Gln, and Lue in the motifs 10, 4, and 1 (SupplementalFigure 6 and Supplemental Figure 7).

3.5. Expression Patterns of Tomato Snf2 Family Genes. Inorder to explore the possible role of tomato snf2s, we ana-lyzed their expression profiles (Figure 6). SlCHR2, SlCHR26,SlCHR8, and SlCHR41 (Snf2-like family) had similar expres-sion profiles and were expressed mainly in roots and fruitsfrom 1 cM to B stages (Figure 6(a)), suggesting that thesegenes may play redundant roles in root and fruit develop-ment. Swr1-like SlCHRs, SlCHR17, and SlCHR19 werestrongly expressed in roots and B+10 stage fruits, whileSlCHR7 was mostly expressed in roots (Figure 6(b)). Interest-ingly, SlCHR10 was expressed in roots and in the early stagesof fruit development (Figure 6(b)). Most of the SSO1653-likeand Distant SlCHR genes accumulated in the early stages offruit development and roots (Figures 6(d) and 6(f)). Accord-ing to the expression profile of Rad54-like and Rad5/16-like

SlCHRs, these SlCHRs could be categorized into twogroups: high expression and low expression (Figures 6(c)and 6(e)). However, some SlCHR genes showed specificexpression peaks. For example, SlCHR9, SlCHR38, andSlCHR40 were strongly expressed in fruits at the 3 cM stage,SlCHR4 and SlCHR5 in buds, while SlCHR28 and SlCHR43in roots (Figures 6(c) and 6(e)). In contrast, SlCHR30,SlCHR34, and SlCHR35 were not detected in all tissuesanalyzed (Figure 6).

We further investigated the expression pattern of SlCHRgenes responding to environmental stimuli including hor-mones, salt, and cold by qRT-PCR. All of the genes analyzedwere clearly repressed by SA and cold treatment, especiallySlCHR27 (Figure 7). Most of the genes analyzed exceptSlCHR14 were induced by ABA and salt treatments. In par-ticular, SlCHR7 and SlCHR17 were strongly induced byABA and salt treatment, respectively (Figure 7). These resultsrevealed that these SlCHR genes may be involved in responseto different environmental stimuli in tomato.

SICHR45Chd1Mi-2

Iswi

Lsh

Snf2

Swr1Ino80

Etl1EP400Mot1

ERCC6

Rad54

ATRXJBP2

DRD1

SMARCAL1

SHPRH

Ris1

Rad5/16

Rad5/16-like

Rad54-like

SSO1653-like

Swr1-like

Snf2-like

Distant

SICHR27SICHR33

SICHR2SICHR26SICHR14SICHR13

SICHR8SICHR41

SICHR6SICHR17SICHR19SICHR10

SICHR7SICHR36SICHR39

SICHR3SICHR22SICHR32SICHR20SICHR25

SICHR9SICHR34SICHR35SICHR11SICHR37SICHR21

SICHR1SICHR38

SICHR4SICHR5

SICHR18

SICHR40SICHR44

SICHR12SICHR16SICHR24SICHR23SICHR31SICHR30SICHR28SICHR29SICHR15SICHR42SICHR43

Figure 3: Exon-intron structures of SlCHR genes. Introns are represented by lines. Exons are indicated by green boxes, while UTR is indicatedby gray boxes.

8 International Journal of Genomics

4. Discussion

Snf2 family proteins are the catalytic subunit of the ATPasechromatin-remodeling complexes and contain highly con-served SNF2-N (DEAD) and helicase-C (HELICs) domainsinvolved in many aspects of DNA events such as transcrip-tion, replication, homologous recombination, and DNArepair [6, 7]. In this study, we systematically identified 45genes encoding Snf2 proteins (SlCHRs) in tomato (Solanumlycopersicum), which are distributed on 11 chromosomes(Table 1 and Figure 1). Eight pairs of SlCHR intrachromoso-mal duplication were identified, indicating that gene duplica-tion may play an important role in SlCHR gene expansion intomato (Table 2 and Supplemental Figure 1). Similar resultswere also reported in other organisms such as human andArabidopsis [55, 56]. The intron phases were similar inSlCHRs and AtCHRs (Supplemental Figure 3), indicatingthat plant Snf2 genes originate from a common ancestor.

Previously, a number of genes encoding Snf2 proteins havebeen identified in Arabidopsis [22], rice [57], and tomato[46]. Nevertheless, only the members of DRD1 and Snf2subfamilies were identified in tomato previously [46].Consistent with the previous report, 3 members of Snf2,SlCHR8 (Solyc01g079690), SlCHR41 (Solyc11g062010),and SlCHR6 (Solyc01g094800), were identified. In addition,other three members, SlCHR34, SlCHR35, and SlCHR40,belonging to the DRD1 subfamily, were also found (Table 1).

Sequence comparative analysis of tomato SlCHRs andArabidopsis AtCHRs revealed some conserved features.For example, all deduced CHRs contained the highly con-served helicase-C domain with about 80 amino acid resi-dues (Figure 5, Supplemental Figure 6 and SupplementalFigure 7). Unlike the members of the human Snf2subfamily, the three Snf2 subfamily proteins (SlCHR8,SlCHR41, and SlCHR6) in tomato lack the conserved HSAdomain (Figure 5). Nevertheless, like the HSA domain of

1-10

0

101-

200

201-

300

301-

400

401-

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501-

600

601-

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701-

800

801-

900

901-

1000

1001

-150

0

1501

-200

0

>200

1

0.40

0.35

0.30

0.25

Freq

uenc

y of

exon

s

0.20

0.15

0.10

0.05

0.00

AtCHRs

SICHRs

(a)

AtCHRs

SICHRs

0.16

0.14

0.12

0.10

Freq

uenc

y of

exon

s

0.08

0.06

0.04

0.02

0.00

1-20

21-4

041

-60

61-8

081

-100

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-200

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>200

1

AtCHRs

SICHRs

0.5

Freq

uenc

y of

intro

ns

0.4

0.3

0.2

0.1

0.0

(c)

AtCHRs

SICHRs

1-20

21-4

041

-60

61-8

081

-100

101-

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121-

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0.30

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Freq

uenc

y of

intro

ns

0.20

0.15

0.10

0.05

0.00

(d)

Figure 4: Size distribution of exons and introns inAtCHRs and SlCHRs. (a) Size distribution of exons inAtCHRs and SlCHRs, (b) detailed sizedistribution of small exons in AtCHRs and SlCHRs, (c) size distribution of introns in AtCHRs and SlCHRs, and (d) detailed size distribution ofsmall introns in AtCHRs and SlCHRs.

9International Journal of Genomics

yeast and human Snf2 proteins, the N-terminal of tomatoSnf2 CHRs also has the conserved amino acid residues E,H, and L (Supplemental Figure 5). As the primary bindingplatform for nuclear actin-related proteins (ARPs) andactin, the HSA domain is important for the activity ofchromatin-remodeling ATPases in yeast and animals [58].Indeed, the ARPs are conserved subunits of the SWI/SNFand INO80 chromatin-remodeling complexes that associatedirectly with the ATPase via the HSA domain [58]. Thebromodomain was first identified in BRM, the Drosophilahomolog of SWI2/SNF2, binding acetylated residues onhistone tails [59]. Therefore, SlCHR8 may be the ATPaseof at least one of the putative SWI/SNF complexes intomato. Additional domains such as HAS and SANT thatfacilitate interaction with the other proteins, as well asbromodomain, chromodomain, and PHD domains thatmodified histones, were also found in SlCHRs (Figure 5).

Previous reports showed that AtCHRs played key roles ina variety of developmental processes in Arabidopsis. Forexample, the AtCHR2 (BRM) was involved in morphologicaltraits of leaves and roots as well as reproduction [27, 28, 31,32, 60]. The stem cell pool maintenance of the apical meri-stem was controlled by AtCHR3 (SYD) [23]. The brassinos-teroid and gibberellin signaling pathways were regulatedby AtCHR6 (PICKLE) during skotomorphogenic growth[42]. Furthermore, AtCHR2 (AtBRM) also acts as a positive

regulator in GA biosynthesis, which regulates GA-responsivegenes in a DELLA-independent manner [61]. AtCHR13(PIE) and AtCHR1 (DDM1) are involved in DNA repairand DNA methylation [62, 63]. A recent study in tomatoshowed that constitutively overexpressed SlCHR8 caused sig-nificantly shorter roots and hypocotyls with reduced cotyle-don size in transgenic tomato plants (cv. Micro-Tom) [47].In this study, we found that many protein motifs such asmotifs 13, 16 20, 7, 8, and 18 in the DRD1 subfamily andmotifs 17, 14, 15, and 19 in the Rad5/16-like family areunique to or mainly exist in one group of SlCHRs (Table 3),indicating that the same group SlCHRsmay play similar rolesas their Arabidopsis counterparts. The expression profilesof SlCHRs indicated that some SlCHRs may play differentroles compared with their homologs in Arabidopsis. Forinstance, SlCHR8 was mainly expressed in roots and fruits(Figure 6(a)), indicating that it may function in root andfruit development, which is consistent with the report thatoverexpression of SlCHR8 in tomato resulted in consider-ably compacter growth including significantly shorter rootsand hypocotyls as well as reduced cotyledon and fruit size[47]. In contrast, its Arabidopsis homolog BRM (AtCHR2)functions in leaf and flower development [27, 31, 60]. Fur-thermore, functional divergence was observed betweenSlCHR41 and its homolog AtCHR3 (SYD), since SlCHR41is poorly expressed in flowers while AtCHR3 is highly

SICHR45Chd1Mi-2

Iswi

Lsh

Snf2

Snf2-like

SICHR27SICHR33

SICHR2SICHR26SICHR14SICHR13

SICHR8SICHR41

SICHR6Swr1

Ino80Etl1

EP400Mot1

ERCC6

Rad54ATRX

JBP2

DRD1

SMARCAL1

Rad54-like

SSO1653-like

Swr1-like

Distant

SICHR17SICHR19SICHR10

SICHR7SICHR36SICHR39

SICHR3SICHR22SICHR32SICHR20SICHR25

SICHR9SICHR34SICHR35SICHR11SICHR37SICHR21

SICHR1SICHR38

SICHR4SICHR5

SICHR18SICHR44

SHPRH

Ris1

Rad5/16

Rad5/16-like

SICHR40SICHR12SICHR16SICHR24SICHR23SICHR31SICHR30SICHR28SICHR29SICHR15SICHR42SICHR43

SNF2-NHelicase-CHANDSANTSLIDEChromo

BROMOHSADBINODUF3535RINGHIRAN

DUF4208PHDDUF1087DUF1086

QLQSnAC

UBAFBOXHNH

100aa

Figure 5: Domain architectures of tomato Snf2 family proteins. Different domains are showed by a rectangle with different colors andnumbers. The scale represents the length of the protein and all proteins are displayed in proportion.

10 International Journal of Genomics

expressed in this organ (Figure 6(a)). Both SlCHR4 andSlCHR5 show a peak expression in buds (Figure 6(c)),indicating a role in gamete and/or flower development.

In addition, we found that some SlCHRs respond to envi-ronmental stimuli. For instance, the expression of mostSlCHRs is repressed by SA but enhanced by ABA

Table 3: Schematic distribution of conserved motifs of SlCHRs.

Helicase_Cdomain

SlCHR45 12 3 5 9 2 14 6 10 4 1 11

SlCHR27 12 3 5 9 2 14 6 10 4 1 11

SlCHR33 12 3 5 9 2 14 6 10 4 1

SlCHR2 12 3 5 9 2 14 6 10 4 1 11

SlCHR26 12 3 5 9 2 14 6 10 4 1 11

SlCHR14 12 3 5 9 2 14 6 10 4 1 11

SlCHR13 12 3 5 9 2 14 6 10 4 1 11

SlCHR8 12 3 5 9 2 14 6 10 4 1

SlCHR41 12 3 5 9 2 14 6 10 4 1 11

SlCHR6 12 3 5 9 2 14 6 10 4 1 11

SlCHR17 12 3 5 9 2 14 6 10 4 1 11

SlCHR19 12 3 5 9 2 14 6 10 4 1 11

SlCHR10 12 3 5 9 2 14 6 10 4 1 11

SlCHR7 12 3 5 9 2 14 6 10 4 1 11

SlCHR36 12 3 5 9 2 14 6 10 4 1 11

SlCHR39 12 3 5 9 2 14 6 10 4 1 11

SlCHR3 12 3 5 9 2 14 6 10 4 1 11

SlCHR22 6 10 4 1 11

SlCHR32 12 3 5 9 2 14 6 10 4 1 11

SlCHR20 12 3 5 9 2 14 6 10 4 1 11

SlCHR25 3 5 9 2 14 6 10 4 1 11

SlCHR9 12 3 5 9 2 14 6 10 4 1 11

SlCHR34 3 5 16 2 7 8 6 10 4 1 11 18

SlCHR35 12 16 20 2 8 6 4 1

SlCHR11 13 12 3 5 16 20 9 2 7 8 6 10 4 1 11 18

SlCHR37 13 12 3 5 16 20 9 2 7 8 6 10 4 1 11 18

SlCHR21 13 12 3 5 16 20 9 2 7 8 6 10 4 1 11 18

SlCHR1 13 12 3 5 16 20 9 2 7 8 6 10 4 1 11 18

SlCHR38 13 12 3 5 16 20 9 2 7 8 6 10 4 1 11 18

SlCHR4 2 7 8 6 10 4 1 11 18

SlCHR5 13 12 3 5 16 20 9 2 7 8 6 10 4 1 11 18

SlCHR44 3 5 9 14 6 10 4 1 11

SlCHR18 12 3 5 9 14 6 10 4 1

SlCHR40 12 3 5 9 19 6 1

SlCHR12 12 3 5 17 9 2 14 15 19 6 10 4 1 11

SlCHR16 12 3 5 17 9 2 14 15 19 6 10 4 1 11

SlCHR24 12 3 5 17 9 2 14 15 19 6 10 4 1 11

SlCHR23 12 3 5 17 9 2 14 15 19 6 10 4 1 11

SlCHR31 12 3 5 17 9 2 14 15 19 6 10 4 1 11

SlCHR30 12 3 5 17 9 2 14 15 19 6 10 4 1

SlCHR28 12 3 5 17 9 2 14 15 19 6 10 4 1

SlCHR29 12 3 5 17 9 2 14 10 4 1

SlCHR15 12 3 5 17 9 2 14 15 19 10 4 1 11

SlCHR42 12 3 5 17 9 2 14 15 19 10 4 1 11

SlCHR43 12 3 5 17 9 2 14 15 19 6 10 4 1 11

11International Journal of Genomics

(Figure 7). In Arabidopsis, CHR2 (BRM) is involved in theABA signaling pathway via binding the regulatory regionsof ABI3 and ABI5 genes [26]. Further Chip-seq analysesshow that BRM-activated genes were primarily enrichedin the categories of jasmonic acid and gibberellic acid

responses, while BRM-repressed genes were primarilyenriched in the categories of salicylic acid and lightresponses [64]. Collectively, these data indicated theimportance of CHRs in plants. Further research isrequired to investigate the molecular mechanism on how

Snf2-like family

0.43B

SICHR45

SICHR27

SICHR33

SICHR2

SICHR26

SICHR13

SICHR14

SICHR8

SICHR41

SICHR6

F L R 1 2 3 MG B B+1065

(a)

Rad5/16-like family

1.1 25

0.05 52

B F L R 1 2 3 MG B B+10

SICHR40

SICHR12

SICHR16

SICHR24

SICHR28

SICHR15

SICHR42

SICHR43

SICHR23

SICHR31

(b)

2.6 23

0 4.6

B F L R 1 2 3 MG B B+10

Rad54-like family

SICHR35

SICHR20

SICHR9

SICHR38

SICHR25

SICHR21

SICHR1

SICHR4

SICHR5

SICHR37

SICHR22

SICHR11

(c)

Swr1-like family

0.26 11B F L R 1 2 3 MG B B+10

SICHR17

SICHR19

SICHR7

SICHR10

(d)

SICHR36

SICHR3

SICHR39

SSO1653-like family

0.98B F L R 1 2 3 MG B B+10

16

(e)

SICHR44

8.80.12

SICHR18

Distant family

B F L R 1 2 3 MG B B+10

(f)

Figure 6: Expression profiles of tomato Snf2s. Heat map of RNA-seq expression data from bud (B), flower (F), leaf (L), root (R), 1cM_fruit(1), 2cM_fruit (2), 3cM_fruit (3), mature green fruit (MG), berry at breaker stage (B), and berry ten days after breaking (B+10). Theexpression values are measured as reads per kilobase of the exon model per million mapped reads (RPKM).

12 International Journal of Genomics

SICHRs are involved in tomato development and hormonesignaling pathways.

5. Conclusions

In this study, a total of 45 full-length SlCHRs were identi-fied in tomato, which are clustered into 6 groups. MostSlCHRs within a group are highly conserved in sequencefeatures, gene structures, and motifs, suggesting the func-tional conservation of SlCHRs within a group. Furthermore,diversities in the specific domains identified in differentgroups indicate that some SlCHRs may have undergonefunctional diversification. The expression profiles suggestthat most SlCHRs are expressed constitutively in tomatoorgans, and RT-qPCR analyses show that the expressionof some SlCHRs is modulated by the exogenous stimuli,suggesting that SlCHRs may play important roles in plantdevelopment and stress responses.

Data Availability

The original data of Snf2-like family proteins are availablefrom ChromDB (http://www.chromdb.org). The sequencesof tomato CHR proteins are available from the InternationalTomato Genome Sequencing Project (https://solgenomics.net/organism/Solanum_lycopersicum/genome).

Conflicts of Interest

The authors declare that there is no conflict of interestregarding the publication of this paper.

Authors’ Contributions

D.Z, S.G., and S.Y. contributed to bioinformatics analyses,performed the qRT-PCR analysis, and participated in writingthe manuscript. J.Y. and P.Y. performed the bioinformaticsanalysis. S.Y., K.W., and S.G. designed the experiment andwrote the manuscript.

Acknowledgments

We are grateful to Dr. Ying Wang (South China BotanicalGarden) for providing the seeds of Solanum lycopersicumcultivar Henz1706. This work was supported by grants fromthe Department of Education of Guangdong Province-Young Creative Talents (Natural Science, no. KA1548818),the Guangdong Natural Science Funds for DistinguishedYoung Scholar (2016A030306047), and the National NaturalScience Foundation of China (no. 31771423).

Supplementary Materials

Supplemental Table 1: sequence features of SlSnf2s in tomatoand Arabidopsis. Gene IDs, protein length, intron number,pI, and molecular weight of Snf2s in A. thaliana and tomatoare shown. Supplemental Table 2: primers used in this study.Supplemental Figure 1: phylogenetic tree of SlCHR proteins.Maximum likelihood phylogenetic tree of predicted proteinsfrom tomato. Bootstrap values higher than 50% are shown.Supplemental Figure 2: neighbor-joining (NJ) phylogenetictree for Snf2s in thaliana (At), rice (Os), and tomato (Sl).The groups of homologous genes identified and bootstrapvalues are shown. The reliability of branching was assessedby the bootstrap resampling method using 1,000 bootstrapreplicates. Supplemental Figure 3: exon-intron structures ofSlCHRs. Introns are represented by lines. Exons are indicatedby green boxes. Intron phases are shown by 0, 1, and 2. Sup-plemental Figure 4: the distribution of intron phases in Snf2sin A. thaliana and tomato. Supplemental Figure 5: sequencecomparison of HSA domain of Snf2 subfamily in plant, yeast,and human. The conserved amino acid residues aremarked inred. Supplemental Figure 6: sequence comparison of helicase_C domain of SlCHRs. The motifs of 10, 4, and 1 are shown.Supplemental Figure 7: sequence logo of the helicase_Cdomain of SlCHRs. (Supplementary Materials)

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tive e

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